different methods to account for population stratification

Question

[mms140130]

Hi,

I think i might be missing something but I have read several articles about accounting for population stratification , using methods like MDS, PCA , EIGENSTART and so on

my question what is the output of these methods, I mean what should I expect by applying this methods , do they provide a better PC's or coordinates that I can add them in the logistic model so to find the relation between the genotype and the phenotype ??

Thanks